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- EMDB-67818: Cryo-EM structure of homotypic CENP-A nucleosome isolated from hu... -

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Entry
Database: EMDB / ID: EMD-67818
TitleCryo-EM structure of homotypic CENP-A nucleosome isolated from human cells
Map data
Sample
  • Complex: Homotypic CENP-A nucleosome extracted from human cells overexpressing CENP-A
    • Complex: nucleosome
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
      • DNA: DNA (131-MER)
    • Complex: CEMP-A
      • Protein or peptide: Histone H3-like centromeric protein A
Keywordsnuclear protein / chromatin / mitosis / centromere
Function / homology
Function and homology information


protein localization to chromosome, centromeric region / CENP-A containing chromatin assembly / condensed chromosome, centromeric region / kinetochore assembly / mitotic cytokinesis / chromosome, centromeric region / mitotic metaphase chromosome alignment / negative regulation of tumor necrosis factor-mediated signaling pathway / pericentric heterochromatin / negative regulation of megakaryocyte differentiation ...protein localization to chromosome, centromeric region / CENP-A containing chromatin assembly / condensed chromosome, centromeric region / kinetochore assembly / mitotic cytokinesis / chromosome, centromeric region / mitotic metaphase chromosome alignment / negative regulation of tumor necrosis factor-mediated signaling pathway / pericentric heterochromatin / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Packaging Of Telomere Ends / Mitotic Prometaphase / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / EML4 and NUDC in mitotic spindle formation / telomere organization / ChAHP complex assembly / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Resolution of Sister Chromatid Cohesion / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / FXIIa activates plasma kallikrein-kinin system / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Meiotic synapsis / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / NuRD complex assembly / Regulation of endogenous retroelements by KRAB-ZFP proteins / Interaction of NuRD complexes with transcription factors / Defective pyroptosis / establishment of mitotic spindle orientation / HDACs deacetylate histones / CHD1 and CHD2 subfamily / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / RHO GTPases Activate Formins / CHD6, CHD7, CHD8, CHD9 subfamily / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / kinetochore / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / HCMV Early Events / Metalloprotease DUBs / nucleosomal DNA binding / innate immune response in mucosa / Separation of Sister Chromatids / structural constituent of chromatin / nucleosome assembly / Regulation of PD-L1(CD274) transcription / UCH proteinases / nucleosome / HATs acetylate histones / E3 ubiquitin ligases ubiquitinate target proteins / killing of cells of another organism / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / Dengue Virus-Host Interactions / antimicrobial humoral immune response mediated by antimicrobial peptide / Senescence-Associated Secretory Phenotype (SASP) / heterochromatin formation / defense response to Gram-negative bacterium / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / negative regulation of cell population proliferation / Amyloid fiber formation
Similarity search - Function
: / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A ...: / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H3-like centromeric protein A / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsTanida E / Hatazawa S / Oishi T / Kobayashi Y / Ogasawara M / Jaskiewicz MA / Takizawa Y / Kurumizaka H
Funding support Japan, 12 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Society for the Promotion of Science (JSPS)JP25K18410 Japan
Japan Society for the Promotion of Science (JSPS)JP25KJ1033 Japan
Japan Society for the Promotion of Science (JSPS)JP26K01945 Japan
Other governmentJPMJER1901 Japan
Other governmentJPMJCR24T3 Japan
Other governmentJPMJSP2108 Japan
Other governmentJP25ama121002 Japan
Other governmentJP25ama121009 Japan
Other private Japan
Other private Japan
Other private Japan
CitationJournal: Commun Biol / Year: 2026
Title: Cryo-EM structures of CENP-A nucleosomes isolated from human cells.
Authors: Eisho Tanida / Suguru Hatazawa / Takumi Oishi / Yuki Kobayashi / Mitsuo Ogasawara / Marta A Jaskiewicz / Akihito Harada / Takeru Fujii / Yasuyuki Ohkawa / Yoshimasa Takizawa / Hitoshi Kurumizaka /
Abstract: Centromeres ensure accurate chromosome segregation, and their identity is specified epigenetically by the histone H3 variant CENP-A. Although the structures of reconstituted CENP-A nucleosomes have ...Centromeres ensure accurate chromosome segregation, and their identity is specified epigenetically by the histone H3 variant CENP-A. Although the structures of reconstituted CENP-A nucleosomes have provided important insights, how this epigenetic mark is structurally organized within native chromatin remains incompletely understood. Here, we combine cryogenic electron microscopy with chromatin immunoprecipitation (ChIP-CryoEM) to determine the structures of human CENP-A nucleosomes isolated directly from cells without crosslinking or stabilizing agents. We resolved two distinct cellular CENP-A nucleosome structures: a homotypic CENP-A nucleosome and a heterotypic CENP-A/H3 nucleosome, which have been proposed to represent centromeric and ectopic nucleosomes, respectively. Both cellular CENP-A nucleosomes assemble as histone octamers and wrap DNA in a left-handed superhelix, supporting an octameric model proposed for native CENP-A chromatin. In addition, the hallmark CENP-A-specific structural features previously characterized in vitro, including the shortened CENP-A N-terminal α-helix and the distinctive RG loop, are preserved in cellular CENP-A nucleosomes. These findings define the structural organization of CENP-A nucleosomes in cellular chromatin.
History
DepositionDec 18, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67818.png

Downloads & links

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Map

FileDownload / File: emd_67818.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.257
Minimum - Maximum-0.81295884 - 1.8314164
Average (Standard dev.)0.005129522 (±0.05616489)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67818_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67818_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homotypic CENP-A nucleosome extracted from human cells overexpres...

EntireName: Homotypic CENP-A nucleosome extracted from human cells overexpressing CENP-A
Components
  • Complex: Homotypic CENP-A nucleosome extracted from human cells overexpressing CENP-A
    • Complex: nucleosome
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
      • DNA: DNA (131-MER)
    • Complex: CEMP-A
      • Protein or peptide: Histone H3-like centromeric protein A

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Supramolecule #1: Homotypic CENP-A nucleosome extracted from human cells overexpres...

SupramoleculeName: Homotypic CENP-A nucleosome extracted from human cells overexpressing CENP-A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: nucleosome

SupramoleculeName: nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#5

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Supramolecule #3: CEMP-A

SupramoleculeName: CEMP-A / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1

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Macromolecule #1: Histone H3-like centromeric protein A

MacromoleculeName: Histone H3-like centromeric protein A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.639531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSRL AREICVKFTR GVDFNWQAQ ALLALQEAAE AFLVHLFEDA YLLTLHAGRV TLFPKDVQLA RRIRGLEEGL GGRILEVLFQ GPHMDYKDDD D KH

UniProtKB: Histone H3-like centromeric protein A

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.165551 KDa
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.935239 KDa
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #5: DNA (131-MER)

MacromoleculeName: DNA (131-MER) / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.547617 KDa
SequenceString: (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN) (DN)(DN)(DN)(DN)(DN)(DN) ...String:
(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 1.25 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6e0p

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 108858
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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